期刊论文详细信息
Journal of Biological Engineering
2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts
J Christopher Anderson3  Angel Asante2  Douglas Densmore1  Jennifer AN Brophy2  Mariana Leguia3 
[1] Current address: Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA;Department of Bioengineering, University of California, Berkeley, CA, 94720, USA;Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
关键词: Synthetic biology;    DNA fabrication;    Automated assembly;    2ab reaction;   
Others  :  806025
DOI  :  10.1186/1754-1611-7-2
 received in 2012-07-24, accepted in 2013-01-01,  发布年份 2013
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【 摘 要 】

There is growing demand for robust DNA assembly strategies to quickly and accurately fabricate genetic circuits for synthetic biology. One application of this technology is reconstitution of multi-gene assemblies. Here, we integrate a new software tool chain with 2ab assembly and show that it is robust enough to generate 528 distinct composite parts with an error-free success rate of 96%. Finally, we discuss our findings in the context of its implications for biosafety and biosecurity.

【 授权许可】

   
2013 Leguia et al.; licensee BioMed Central Ltd.

【 预 览 】
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【 参考文献 】
  • [1]Purnick PE, Weiss R: The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 2009, 10:410-422.
  • [2]Ellis T, Adie T, Baldwin GS: DNA assembly for synthetic biology: from parts to pathways and beyond. Integr Biol (Camb) 2011, 3:109-118.
  • [3]Czar MJ, Anderson JC, Bader JS, Peccoud J: Gene synthesis demystified. Trends Biotechnol 2009, 27:63-72.
  • [4]Tian J, Ma K, Saaem I: Advancing high-throughput gene synthesis technology. Mol Biosyst 2009, 5:714-722.
  • [5]Xiong AS, Peng RH, Zhuang J, Liu JG, Gao F, Chen JM, Cheng ZM, Yao QH: Non-polymerase-cycling-assembly-based chemical gene synthesis: strategies, methods, and progress. Biotechnol Adv 2008, 26:121-134.
  • [6]Bilitchenko L, Liu A, Cheung S, Weeding E, Xia B, Leguia M, Anderson JC, Densmore D: Eugene - a domain specific language for specifying and constraining synthetic biological parts, devices, and systems. PLoS One 2011, 6:e18882.
  • [7]Leguia M, Brophy J, Densmore D, Anderson JC: Automated assembly of standard biological parts. Methods Enzymol 2011, 498:363-397.
  • [8]Anderson JC, Dueber JE, Leguia M, Wu GC, Goler JA, Arkin AP, Keasling JD: BglBricks: A flexible standard for biological part assembly. J Biol Eng 2010, 4:1. BioMed Central Full Text
  • [9]Kim YJ, Bjorklund S, Li Y, Sayre MH, Kornberg RD: A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 1994, 77:599-608.
  • [10]Sato S, Tomomori-Sato C, Parmely TJ, Florens L, Zybailov B, Swanson SK, Banks CA, Jin J, Cai Y, Washburn MP, et al.: A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology. Mol Cell 2004, 14:685-691.
  • [11]Baumli S, Hoeppner S, Cramer P: A conserved mediator hinge revealed in the structure of the MED7.MED21 (Med7.Srb7) heterodimer. J Biol Chem 2005, 280:18171-18178.
  • [12]Salis HM: The ribosome binding site calculator. Methods Enzymol 2011, 498:19-42.
  • [13]Densmore D, Hsiau TH, Kittleson JT, DeLoache W, Batten C, Anderson JC: Algorithms for automated DNA assembly. Nucleic Acids Res 2010, 38:2607-2616.
  • [14]Knight TF Jr: Idempotent vector design for standard assembly of Biobricks. 2003. In DSpace http://hdlhandlenet/17211/21168 webcite
  • [15]Pedelacq JD, Cabantous S, Tran T, Terwilliger TC, Waldo GS: Engineering and characterization of a superfolder green fluorescent protein. Nat Biotechnol 2006, 24:79-88.
  • [16]Engler C, Gruetzner R, Kandzia R, Marillonnet S: Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes. PLoS One 2009, 4:e5553.
  • [17]Gibson DG: Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides. Nucl Acids Res 2009, 37(20):6984-6990.
  • [18]Horton RM: PCR-mediated recombination and mutagenesis. SOEing together tailor-made genes. Mol Biotechnol 1995, 3:93-99.
  • [19]Horton RM, Cai ZL, Ho SN, Pease LR: Gene splicing by overlap extension: tailor-made genes using the polymerase chain reaction. Biotechniques 1990, 8:528-535.
  • [20]Quan J, Tian J: Circular polymerase extension cloning for high-throughput cloning of complex and combinatorial DNA libraries. Nat Protoc 2011, 6:242-251.
  • [21]Quan J, Tian J: Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One 2009, 4:e6441.
  • [22]Callura JM, Cantor CR, Collins JJ: Genetic switchboard for synthetic biology applications. Proc Natl Acad Sci U S A 2012, 109:5850-5855.
  • [23]Bilitchenko L, Liu A, Densmore D: The Eugene language for synthetic biology. Methods Enzymol 2011, 498:153-172.
  • [24]Czar MJ, Cai Y, Peccoud J: Writing DNA with GenoCAD. Nucleic Acids Res 2009, 37:40-47.
  • [25]Smith LP, Bergmann FT, Dhandran D, Sauro HM: Antimony: a modular model definition language. Bioinformatics 2009, 25:2452-2454.
  • [26]Umesh P, Naveen F, Rao CU, Nair AS: Programming languages for synthethic biology. Syst Synth Biol 2010, 4:265-269.
  • [27]Wilson ML, Hertzberg R, Adam L, Peccoud J: A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD. Methods Enzymol 2011, 498:173-188.
  • [28]Galdzicki M, Rodriguez C, Chandran D, Sauro HM, Gennari JH: Standard biological parts knowledgebase. PLoS One 2011, 6:e17005.
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